Extended Data Figure 3. Replicate data for effect of CTCF or cohesin depletion on distal enhancer driven gene activation.

(a) Quantification of the percentage of (left axis) Shh and (right axis) Lmbr1 expressing alleles, assayed by RNA FISH, in TALE-transfected wild type mESCs (parental cell line used to generate the CTCF-AID cell line) and in CTCF-AID cells either untreated (- auxin) or treated with 24 hours of auxin (+ auxin). Cells were transfected with tShh-VP64, tSBE2-VP64 and tZRS-VP64 and equivalent TALE-Δ controls. Data shown are from an indepenent biological replicate of the experiment shown in Fig 3a. The data were compared using a two-sided Fisher’s Exact Test, n = numer of alleles scored, ns – not significant. Source Data EDFig3. (b) As for (a) but for SCC1-AID with 6 hours of auxin (+ auxin). Data shown are from an indepenent biological replicate of the experiment shown in Fig 3b. **p<0.01. Source Data EDFig3. (c) Table showing two-sided Fisher’s Exact Test p-values for differences in the percent of Shh-expressing alleles in TALE-transfected CTCF-AID cells assayed by RNA FISH in the absence or presence of auxin. Cells were transfected with Shh-VP64, SBE2-VP64, ZRS-VP64, and equivalent TALE-Δ controls. Data from Figure 3a and Extended Data Figure 3a. p-values in bold are significant (<0.05). (d) As (c) but for SCC1-AID cells. Data from Figure 3d and Extended Data Figure 3b. (e) Table showing the two-sided Mann-Whitney U p-values for differences in FISH inter-probe distances, for Shh-SBE2, SBE2-ZRS and Shh-ZRS probe pairs, between the data from TALE-Vp64 transfected CTCF-AID or SCC1-AID ESCs with or without the addition of auxin. No of alleles scored is indicated (in parentheses). Data are from Figures 3c and 3f. Median and inter-quartile distances are shown. p-values in bold are significant (<0.05).